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United States Department of Agriculture

Agricultural Research Service

Research Project: IMPROVING GENETIC PREDICTIONS FOR DAIRY ANIMALS USING PHENOTYPIC AND GENOMIC INFORMATION Title: Genomic Selection and its Effects on Dairy Cattle Breeding Programs

Authors
item Weigel, K -
item DE Los Campos, G -
item Vazquez, A -
item Van Tassell, Curtis
item Rosa, G.J.M. -
item Gianola, D -
item O'Connell, J -
item Vanraden, Paul
item Wiggans, George

Submitted to: World Congress of Genetics Applied in Livestock Production
Publication Type: Proceedings
Publication Acceptance Date: June 1, 2010
Publication Date: August 1, 2010
Citation: Weigel, K.A., De Los Campos, G., Vazquez, A.I., Van Tassell, C.P., Rosa, G., Gianola, D., O'Connell, J.R., Van Raden, P.M., Wiggans, G.R. 2010. Genomic Selection and its Effects on Dairy Cattle Breeding Programs. World Congress of Genetics Applied in Livestock Production. 9th World Congr. Genet. Appl. Livest. Prod., Leipzig, Germany, Aug. 1–6, 8 pp.

Interpretive Summary: The availability of high-throughput assays for genotyping single nucleotide polymorphisms (SNP) has led to genomic evaluations replacing traditional evaluation systems used for dairy cattle selection. A review of four different methods indicates that genomic selection using high-density SNP genotypes will greatly enhance genetic progress in dairy cattle. Dairy producers will benefit from the development of low-density assays containing selected SNP with large estimated effects or, more likely, low-density assays containing equally spaced SNP that will facilitate imputation of high-density genotypes which could lead to widespread adoption of genomics on commercial farms. Potential applications include improved selection of replacement heifers on farms that use gender-enhanced semen, preliminary genomic screening of young bulls or potential bull dams, parentage discovery, genome-enhanced mate selection, and genome-guided management protocols.

Technical Abstract: The availability of high-throughput assays for genotyping single nucleotide polymorphisms (SNP) has led to the genotyping of thousands of dairy cattle, mostly progeny tested bulls in artificial insemination programs or young bulls that are candidates for such programs, using the BovineSNP50 BeadChip (Illumina, Inc., San Diego, CA) or similar platforms. Results to date indicate that genomic selection using high-density SNP genotypes will greatly enhance genetic progress in dairy cattle. However, at current prices genotyping may be limited to males and elite females. This paper summarizes four recent studies regarding: 1) the relationship between published, genome-enhanced predicted transmitting abilities (GPTA) and subsequent daughter performance; 2) the predictive ability of direct genomic values (DGV) resulting from selection of low-density SNP based on magnitude of estimated effects; 3) the accuracy of imputation of high-density genotypes from equally spaced low-density SNP, and 4) the precision of DGV derived from imputed high-density genotypes. Low-density assays containing 300 to 1,000 selected SNP with large estimated effects may provide breed and trait-specific DGV or GPTA with sufficient accuracy to allow preliminary screening of selection candidates. However, low-density assays containing 2,000 to 4,000 equally spaced SNP will facilitate accurate imputation of high-density genotypes which, in turn, can be used to compute DGV or GPTA that are only slightly less accurate than estimates derived from actual high-density genotypes. Development of inexpensive, low-density assays could lead to widespread application of genomics on commercial dairy farms, with applications including: selection of replacement heifers on farms that use gender-enhanced semen, preliminary genomic screening of young bulls or potential bull dams, parentage discovery, genome-enhanced mate selection, and genome-guided management protocols.

Last Modified: 7/31/2014